| 1. Round | 09/08/2016 | Deportivo Lara | - | Atlético Junior | 1:3 |  |
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| 1. Round | 17/08/2016 | Atlético Junior | - | Deportivo Lara | 2:1 | ||||
| 2. Round | 24/08/2016 | Blooming | - | Atlético Junior | 0:2 | |
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| 2. Round | 15/09/2016 | Atlético Junior | - | Blooming | 1:1 | ||||
| Round of 16 | 21/09/2016 | Montevideo Wanderers | - | Atlético Junior | 0:0 | ||||
| Round of 16 | 28/09/2016 | Atlético Junior | - | Montevideo Wanderers | 4:3 pso | ||||
| Quarter-finals | 20/10/2016 | Atlético Junior | - | Chapecoense | 1:0 | ||||
| Quarter-finals | 27/10/2016 | Chapecoense | - | Atlético Junior | 3:0 |
Paraguay
Spain